RBAtools is a Python programming interface for the Resource Balance Analysis (RBA) framework. It includes methods to solve, modify, and analyse RBA models and to export model information and simulation results into various formats.
To provide a brief and immediately accessible impression for you, we created an online demo.
Linear solver support:
RBAtools is based on linear programming and therefore requires a linear optimization package. We strongly suggest using the (proprietary) CPLEX tool, which is available under a free academic license. Nonetheless we included functionality with the freely available swiglpk solver. However sometimes this solver is not able to obtain numerically accurate solutions.
Availability:
RBAtools can be obtained from our GitHub page, or from PyPI.
Installation:
When installing the rbatools library, command line tools for basic applications will be co-installed.
Install this package locally:
After cloning this repository, in your terminal navigate into the base directory of rbatools locally on your computer and execute:
pip install .
Install this package from PyPI:
pip install rbatools
Online demo:
We generated a short demo to be accessed online (without any local installations/requirements).
Model availability:
RBA models have already been developed for:
- Bacillus subtilis 168 (wild type)
- Escherichia coli K-12 (wild type)
- CO2-fixing Escherichia coli K-12 (engineered strain)
You can obtain these models here.
Literature:
RBAtools and results are presented in our article.
Authors:
Bodeit, O., Liebermeister, W. and Goelzer A.
Citation:
If you use RBAtools for scientific publications, please cite our article: Bodeit O., Ben Samir I., Karr J.R., Liebermeister W., Goelzer A. (2023), "RBAtools: a programming interface for Resource Balance Analysis models", Bioinformatics Advances 3 (2023). https://doi.org/10.1093/bioadv/vbad056
License:
Copyright (c) 2022 INRAE - MaIAGE - France.
rbatools is a free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. rbatools is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with rbatools. If not, see https://www.gnu.org/licenses